mTAIL-seq reveals dynamic poly(A) tail regulation in oocyte-to-embryo development

Here, Lim et al. report a new version of TAIL-seq (mRNA TAIL-seq [mTAIL-seq]) with enhanced sequencing depth for mRNAs (by ∼1000-fold compared with the previous version). Using their new methodology, the authors investigated mRNA tailing in Drosophila oocytes and embryos and demonstrated a relationship between poly(A) tail length and translational efficiency during egg activation.

[1]  D. Patel,et al.  Uridylation by TUT4 and TUT7 Marks mRNA for Degradation , 2014, Cell.

[2]  D. Patel,et al.  Adenylation of maternally inherited microRNAs by Wispy. , 2014, Molecular cell.

[3]  S. Dudoit,et al.  Normalization of RNA-seq data using factor analysis of control genes or samples , 2014, Nature Biotechnology.

[4]  D. Bartel,et al.  Widespread changes in the posttranscriptional landscape at the Drosophila oocyte-to-embryo transition. , 2014, Cell reports.

[5]  B. Tian,et al.  Sizing up the poly(A) tail: insights from deep sequencing. , 2014, Trends in biochemical sciences.

[6]  V. Kim,et al.  TAIL-seq: genome-wide determination of poly(A) tail length and 3' end modifications. , 2014, Molecular cell.

[7]  D. Bartel,et al.  Poly(A)-tail profiling reveals an embryonic switch in translational control , 2014, Nature.

[8]  L. Ovchinnikov,et al.  Poly(A)-binding proteins: Structure, domain organization, and activity regulation , 2013, Biochemistry (Moscow).

[9]  M. Wolfner,et al.  Cytoplasmic polyadenylation is a major mRNA regulator during oogenesis and egg activation in Drosophila. , 2013, Developmental biology.

[10]  C. Norbury Cytoplasmic RNA: a case of the tail wagging the dog , 2013, Nature Reviews Molecular Cell Biology.

[11]  A. D’Ambrogio,et al.  Translational control of cell growth and malignancy by the CPEBs , 2013, Nature Reviews Cancer.

[12]  Ian M. Dobbie,et al.  Drosophila patterning is established by differential association of mRNAs with P bodies , 2012, Nature Cell Biology.

[13]  Vanessa L. Horner,et al.  Protein phosphorylation changes reveal new candidates in the regulation of egg activation and early embryogenesis in D. melanogaster. , 2012, Developmental biology.

[14]  R. Zukin,et al.  Bidirectional control of mRNA translation and synaptic plasticity by the cytoplasmic polyadenylation complex. , 2012, Molecular cell.

[15]  Felice-Alessio Bava,et al.  Translational control by changes in poly(A) tail length: recycling mRNAs , 2012, Nature Structural &Molecular Biology.

[16]  A. Giraldez,et al.  Ribosome Profiling Shows That miR-430 Reduces Translation Before Causing mRNA Decay in Zebrafish , 2012, Science.

[17]  T. Orr-Weaver,et al.  Developmental control of oocyte maturation and egg activation in metazoan models. , 2011, Cold Spring Harbor perspectives in biology.

[18]  D. Montell,et al.  Shining light on Drosophila oogenesis: live imaging of egg development. , 2011, Current opinion in genetics & development.

[19]  Colin N. Dewey,et al.  RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.

[20]  Christophe Dessimoz,et al.  Base-calling for next-generation sequencing platforms , 2011, Briefings Bioinform..

[21]  Javier Gallego,et al.  Mitotic cell-cycle progression is regulated by CPEB1 and CPEB4-dependent translational control , 2010, Nature Cell Biology.

[22]  G. Bussotti,et al.  A novel, noncanonical mechanism of cytoplasmic polyadenylation operates in Drosophila embryogenesis. , 2010, Genes & development.

[23]  Wael Tadros,et al.  The maternal-to-zygotic transition: a play in two acts , 2009, Development.

[24]  Irina I. Abnizova,et al.  Swift: primary data analysis for the Illumina Solexa sequencing platform , 2009, Bioinform..

[25]  Nicholas T. Ingolia,et al.  Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling , 2009, Science.

[26]  R. Hawley,et al.  Mutations in the Chromosomal Passenger Complex and the Condensin Complex Differentially Affect Synaptonemal Complex Disassembly and Metaphase I Configuration in Drosophila Female Meiosis , 2009, Genetics.

[27]  L. Vardy,et al.  Regulation of Cyclin A protein in meiosis and early embryogenesis , 2009, Proceedings of the National Academy of Sciences.

[28]  M. Wickens,et al.  PAP- and GLD-2-type poly(A) polymerases are required sequentially in cytoplasmic polyadenylation and oogenesis in Drosophila , 2008, Development.

[29]  Vanessa L. Horner,et al.  Wispy, the Drosophila Homolog of GLD-2, Is Required During Oogenesis and Egg Activation , 2008, Genetics.

[30]  Vanessa L. Horner,et al.  Transitioning from egg to embryo: Triggers and mechanisms of egg activation , 2008, Developmental dynamics : an official publication of the American Association of Anatomists.

[31]  R. Guigó,et al.  A Combinatorial Code for CPE-Mediated Translational Control , 2008, Cell.

[32]  T. Gant,et al.  A novel method for poly(A) fractionation reveals a large population of mRNAs with a short poly(A) tail in mammalian cells , 2007, Nucleic acids research.

[33]  T. Preiss,et al.  Widespread use of poly(A) tail length control to accentuate expression of the yeast transcriptome. , 2007, RNA.

[34]  J. Richter,et al.  CPEB: a life in translation. , 2007, Trends in biochemical sciences.

[35]  J. Richter,et al.  Opposing polymerase-deadenylase activities regulate cytoplasmic polyadenylation. , 2006, Molecular cell.

[36]  E. Wahle,et al.  An essential cytoplasmic function for the nuclear poly(A) binding protein, PABP2, in poly(A) tail length control and early development in Drosophila. , 2005, Developmental cell.

[37]  J. Richter,et al.  Activity-dependent polyadenylation in neurons. , 2005, RNA.

[38]  M. Wickens,et al.  Mammalian GLD-2 homologs are poly(A) polymerases. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[39]  A. Ephrussi,et al.  PKA-R1 spatially restricts Oskar expression for Drosophila embryonic patterning , 2004, Development.

[40]  A. Ephrussi,et al.  Orb and a long poly(A) tail are required for efficient oskar translation at the posterior pole of the Drosophila oocyte , 2003, Development.

[41]  R. Méndez,et al.  Translational control by CPEB: a means to the end , 2001, Nature Reviews Molecular Cell Biology.

[42]  M. Wolfner,et al.  Male contributions to egg production: the role of accessory gland products and sperm in Drosophila melanogaster , 2001, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[43]  E. Wahle,et al.  The biochemistry of polyadenylation. , 1996, Trends in biochemical sciences.

[44]  P. Macdonald,et al.  Translational regulation of oskar mRNA by Bruno, an ovarian RNA-binding protein, is essential , 1995, Cell.

[45]  J. Gergen,et al.  Coordinate initiation of Drosophila development by regulated polyadenylation of maternal messenger RNAs. , 1994, Science.

[46]  M. Wickens,et al.  The 3'-untranslated regions of c-mos and cyclin mRNAs stimulate translation by regulating cytoplasmic polyadenylation. , 1994, Genes & development.

[47]  A. Mahowald,et al.  tudor, a gene required for assembly of the germ plasm in Drosophila melanogaster , 1985, Cell.

[48]  J. Laver,et al.  Regulation and Function of Maternal Gene Products During the Maternal-to-Zygotic Transition in Drosophila. , 2015, Current topics in developmental biology.

[49]  Paul Theodor Pyl,et al.  HTSeq – A Python framework to work with high-throughput sequencing data , 2014, bioRxiv.

[50]  G. McNeil,et al.  Drosophila Oogenesis , 2015, Methods in Molecular Biology.

[51]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[52]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[53]  L. Vardy,et al.  The Drosophila PNG kinase complex regulates the translation of cyclin B. , 2007, Developmental cell.

[54]  Timothy R Hughes,et al.  SMAUG is a major regulator of maternal mRNA destabilization in Drosophila and its translation is activated by the PAN GU kinase. , 2007, Developmental cell.

[55]  W. Richards,et al.  Assaying the polyadenylation state of mRNAs. , 1999, Methods.